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Armed conflict between the government and the Lord's Resistance Army (LRA) broke out in northern Uganda in 1988, causing large-scale displacement. LRA attacks on civilians forced many to flee their homes, and in 1996 the government began to forcibly relocate people from the Acholi region into camps described as "protected villages". By the end of 2005, around 1.8 million people had been moved. An unknown number fled to urban areas in other parts of Uganda, where they have been largely unacknowledged and unassisted.

The signing of a cessation of hostilities agreement in 2006 improved security and led to the return or settlement elsewhere of most IDPs living in camps. A shortfall in recovery and development efforts however, means the majority of returnees still struggled to access basic services during 2012. The return process has also been marred by land conflicts, sometimes leading to violence and secondary displacement.

No new assessment was carried out in 2012, therefore the number of IDPs in Uganda is still estimated to be about 30,000. The vast majority continue to live in dismantled camps and transit sites, and rely on the basic services available in neighbouring villages. They are unable to return either because of age, illness or disability, or because they have no access to land. The figure of 30,000 does not include IDPs living with rural host communities or in urban areas.

Uganda is party to the Great Lakes Pact and became the first country to ratify the Kampala Convention in 2010. It adopted a national policy on IDPs in 2004 and started to implement the Peace, Recovery and Development Plan for Northern Uganda in 2008. Despite considerable investment, however, the plan has had only a limited impact in enabling durable solutions. Donors withheld hundreds of millions of dollars in aid in 2012, following allegations of large-scale embezzlement by officials.